The meeting had been billed as a showdown. In reality, it had more the flavor of two opponents sizing each other up. Afterward, the Vatican press office described the encounter, between top officials in the Catholic Church and a group of American nuns the Vatican has accused of straying from official Catholicism, as having taken place “in an atmosphere of openness and cordiality.” For the nuns, representatives of the Leadership Conference of Women Religious (LCWR), an umbrella organization that represents some 80% of Catholic nuns in the U.S., the meeting was “an opportunity to express our concerns” directly to officials at the Congregation for the Doctrine of the Faith (CDF), the Vatican office charged with policing church doctrine now headed by the American Cardinal William Levada.

It’s not surprising that little was decided. The standoff is a long-standing one, dating back to the period following the Second Vatican Council in the 1960s, when the Holy See instituted a series of reforms and liberalizations, among them a call for religious orders, including nuns, to renew themselves. In the following years, many orders began allowing their members to shed the severe habits that date back to medieval times, to work outside of traditional church institutions, like schools and hospitals. Increasingly, nuns began to get involved in social movements, joining the battles for civil rights, setting up AIDS hospices and launching antipoverty campaigns. “Suddenly the lid was off,” says Kenneth Briggs, author of Double Crossed: Uncovering the Catholic Church’s Betrayal of American Nuns. “Sisters were deciding for themselves what to do. And back at headquarters, the Vatican and bishops in particular got very nervous.”

For the Vatican, the rebel nuns present a delicate challenge. In the U.S., many nuns find themselves politically on the opposite side of the church hierarchy, for instance during the health care debate, when they lent support to President Obama’s policies. Though nuns don’t have a formal position within the Vatican’s ranks — unlike, say, priests, they are considered laypeople — they are nonetheless an important part of the church’s public and popular face. And since their orders are nearly always self-funded, the Vatican has little traction, outside of theological condemnation, in reining them in.

At issue is not only the role that nuns should play within the greater dialogue of the Catholic faith, but what direction the church itself should be headed, with Pope Benedict XVI one of the primary advocates of rolling back reforms in favor of a return toward traditional Catholicism. “The critique of the LCWR is a microcosm of a larger phenomenon in the church, specifically over how deeply the Second Vatican Council represented a break with the past,” says James Martin, a Jesuit priest and contributing editor at America, a Catholic magazine.

In recent months, the conflict has escalated. In March, an association of American bishops criticized a book by a nun, Sister Elizabeth Johnson, which explores the idea of God from feminist, black, Hispanic, interreligious and ecological viewpoints. Last week, the CDF condemned a book by another American nun named Sister Margaret Farley, which tackles sexual ethics, including same-sex relationships, divorce, masturbation and remarriage.

In a report released in April, the Vatican accused the LCWR of having fostered theological dissent among its members, in particular on issues of homosexuality, and of promoting what the authors of the report called “radical feminist themes incompatible with the Catholic faith.” A reform of the organization was ordered, and an Archbishop was put in charge of implementing it. In response, the nuns issued a statement in June claiming the report “was based on unsubstantiated accusations and the result of a flawed process that lacked transparency,” and said the Vatican’s actions had “caused scandal and pain throughout the church community and created greater polarization.”

Yet if anybody blinked during Tuesday’s meeting, it was behind closed doors. Afterward, the Vatican, in its statement, stressed that it considered the group to be “under the supreme direction of the Holy See” and thus, subject to its authority. Sister Pat Farrell, the president of the LCWR, restated the group’s intention to determine its next course of action in an assembly in August. The options will be few: to somehow accommodate the Vatican’s demands, or — as Farrell has said could be possible — to break with Rome completely. Compromise seems an unlikely option. Says Briggs: “The Vatican doesn’t have a history of saying, ‘You know what? You’re right. We had it wrong.'”